#!/bin/bash

files='RGc19_S11 RGc18_S10 RGc16_S8 RGc20_S12 RGc14_S6 RGc15_S7 RGc17_S9'

for f in $files; do
    echo $f;
    alevin-fry generate-permit-list --input ../outputs/salmon_alevin/${f}/ --expected-ori fw --output-dir ../outputs/alevin_fry_gpl/${f} --unfiltered-pl ../ref_files/3M-february-2018.cleaned.txt;
    echo '';
done
